BN1204 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 1.9462e-06 1.2901e-04
Layer 5 1.6306e-05 5.3852e-04
Layer 3 4.4926e-05 1.2447e-03
Layer 2 2.2844e-04 3.9067e-02
Layer 6 4.0132e-04 2.3775e-03
Layer 1 1.8966e-03 3.9354e-02
WM 4.2760e-03 8.1381e-02

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 1.9741 0.6164
ATP6V0A1 Layer 4 2.6367 0.5755
DNM1 Layer 4 3.1523 0.5669
KIF1A Layer 3 2.6895 0.5651
TUBA1B Layer 5 2.6191 0.5640
DGKZ Layer 5 2.5273 0.5556
SLC17A7 Layer 6 2.9961 0.5547
RTN1 Layer 4 2.6309 0.5537
MAP2 Layer 5 2.7480 0.5505
MAP1B Layer 5 2.4609 0.5497
EEF2 Layer 3 2.4971 0.5472
VAMP2 Layer 5 2.8711 0.5453
ATP6V0C Layer 5 2.4883 0.5422
MAP1A Layer 4 2.7715 0.5418
LMO4 Layer 4 2.9414 0.5416
CEND1 Layer 5 2.4941 0.5405
CALM3 Layer 5 2.8281 0.5393
NORAD Layer 4 2.5059 0.5393
MAPK8IP2 Layer 5 2.6016 0.5391
UCHL1 Layer 4 3.3789 0.5387
MTCH1 Layer 3 2.3496 0.5384
BASP1 Layer 4 3.1934 0.5375
EEF1A2 Layer 6 2.4668 0.5350
HSP90AB1 Layer 5 2.5059 0.5332
ARL6IP1 Layer 5 2.5332 0.5317
APBB1 Layer 5 2.1582 0.5316
C5orf63 Layer 3 2.1543 0.5312
SNAP25 Layer 4 2.9863 0.5304
FAIM2 Layer 5 2.6660 0.5297
CPLX1 Layer 4 2.7422 0.5287
CAMK2B Layer 6 2.6426 0.5262
NRGN Layer 4 2.6895 0.5253
TSPYL1 Layer 5 2.5449 0.5250
GPM6A Layer 4 2.4180 0.5249
SCAMP5 Layer 5 2.2930 0.5248
GAP43 Layer 4 2.5059 0.5233
NECAB1 Layer 4 2.3926 0.5232
TLE5 Layer 5 2.4512 0.5225
SELENOW Layer 4 2.4180 0.5211
ACO2 Layer 5 2.2266 0.5201
SYN2 Layer 4 2.6484 0.5166
PSAP Layer 4 2.9219 0.5131
SNCB Layer 4 3.0195 0.5128
THY1 Layer 6 2.4668 0.5126
IDS Layer 4 2.4238 0.5104
STMN2 Layer 5 2.4512 0.5080
DDAH1 Layer 4 2.4844 0.5076
MIF Layer 5 2.3750 0.5061
PRKCB Layer 2 2.5273 0.5043
TPI1 Layer 4 2.8027 0.5032

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1204
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1204_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1204/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1204/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1204/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1204/report/PD/BN1204_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1204/report/PD/BN1204_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 02:41:45
  • Number of Processes: 10
  • Spending Time: 0h 3m